These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

173 related articles for article (PubMed ID: 18683966)

  • 1. FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins.
    Vorobjev YN; Vila JA; Scheraga HA
    J Phys Chem B; 2008 Sep; 112(35):11122-36. PubMed ID: 18683966
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.
    Vorobjev YN; Almagro JC; Hermans J
    Proteins; 1998 Sep; 32(4):399-413. PubMed ID: 9726412
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins.
    Vorobjev YN; Scheraga HA; Vila JA
    J Biomol Struct Dyn; 2018 Feb; 36(3):561-574. PubMed ID: 28132613
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Self-consistent field approach to protein structure and stability. I: pH dependence of electrostatic contribution.
    Dimitrov RA; Crichton RR
    Proteins; 1997 Apr; 27(4):576-96. PubMed ID: 9141137
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure.
    van Vlijmen HW; Schaefer M; Karplus M
    Proteins; 1998 Nov; 33(2):145-58. PubMed ID: 9779784
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation.
    Pokala N; Handel TM
    Protein Sci; 2004 Apr; 13(4):925-36. PubMed ID: 15010542
    [TBL] [Abstract][Full Text] [Related]  

  • 7. On the pH dependence of protein stability.
    Yang AS; Honig B
    J Mol Biol; 1993 May; 231(2):459-74. PubMed ID: 8510157
    [TBL] [Abstract][Full Text] [Related]  

  • 8. p
    Aleksandrov A; Roux B; MacKerell AD
    J Chem Theory Comput; 2020 Jul; 16(7):4655-4668. PubMed ID: 32464053
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements.
    Altman MD; Bardhan JP; White JK; Tidor B
    J Comput Chem; 2009 Jan; 30(1):132-53. PubMed ID: 18567005
    [TBL] [Abstract][Full Text] [Related]  

  • 10. A detailed representation of electrostatic energy in prediction of sequence and pH dependence of protein stability.
    Dudek MJ
    Proteins; 2014 Oct; 82(10):2497-511. PubMed ID: 24863377
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes.
    Alexov E
    Proteins; 2004 Aug; 56(3):572-84. PubMed ID: 15229889
    [TBL] [Abstract][Full Text] [Related]  

  • 12. A two level hierarchical model of protein retention in ion exchange chromatography.
    Salvalaglio M; Paloni M; Guelat B; Morbidelli M; Cavallotti C
    J Chromatogr A; 2015 Sep; 1411():50-62. PubMed ID: 26278361
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
    Georgescu RE; Alexov EG; Gunner MR
    Biophys J; 2002 Oct; 83(4):1731-48. PubMed ID: 12324397
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins.
    Avbelj F
    J Mol Biol; 2000 Jul; 300(5):1335-59. PubMed ID: 10903873
    [TBL] [Abstract][Full Text] [Related]  

  • 15. A fast and simple method to calculate protonation states in proteins.
    Sandberg L; Edholm O
    Proteins; 1999 Sep; 36(4):474-83. PubMed ID: 10450090
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.
    Aleksandrov A; Lin FY; Roux B; MacKerell AD
    J Comput Chem; 2018 Aug; 39(22):1707-1719. PubMed ID: 29737546
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.
    Marenich AV; Cramer CJ; Truhlar DG
    J Phys Chem B; 2009 May; 113(18):6378-96. PubMed ID: 19366259
    [TBL] [Abstract][Full Text] [Related]  

  • 18. pH-dependent stability of sperm whale myoglobin in water-guanidine hydrochloride solutions.
    Shosheva A; Miteva M; Christova P; Atanasov B
    Eur Biophys J; 2003 Feb; 31(8):617-25. PubMed ID: 12582821
    [TBL] [Abstract][Full Text] [Related]  

  • 19. [Molecular dynamics method for proteins with ionization-conformation coupling and equilibrium titration].
    Vorob'ev IuN
    Mol Biol (Mosk); 2011; 45(2):346-55. PubMed ID: 21634122
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.
    Izadi S; Aguilar B; Onufriev AV
    J Chem Theory Comput; 2015 Sep; 11(9):4450-9. PubMed ID: 26575935
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.